Programmatic Retrieval of Small Molecule Information from PubChem Using PUG-REST

PubChem ( https://pubchem.ncbi.nlm.nih.gov ) is an open archive which contains information on small molecules as well as other chemical entities such as lipids, carbohydrates, and (chemically modified) amino acid and nucleic acid sequences (including siRNA and miRNA). Developed and maintained by the US National Institutes of Health, PubChem is a chemical information hub, collecting chemical information from various data sources and disseminating it to the public free of charge. PubChem provides multiple programmatic access routes, including E-Utilities, Power User Gateway (PUG), PUG-SOAP, and PUG-REST. This chapter describes how to access PubChem programmatically through PUG-REST. The syntax of the PUG-REST request URL is explained with many examples that cover various tasks and a series of Perl scripts are provided to demonstrate how these URLs can be included in actual programs.